The rules state that, unless the referee is asked, conversions must be kicked with the same ball that was used to score the try.
However, the England staff did not consult the referee whether it was okay to change the balls for the kicks.
"I'm an employee of the RFU," said Johnson. "Paul and David did what they did in the heat and confusion of a Test match.
"I don't suspend guys lightly. We regret what we did and it was wrong. They have made a mistake and paid for it.
"We should have asked the referee [to switch the ball]. We didn't. They asked us to stop. We did."
England must avoid defeat by eight points against Scotland on Saturday in order to progress to the World Cup quarter-finals.